Meat department manager Kevin Morlan arranges packages of meat at a Dahl's grocery store in Des Moines, Iowa, last month. A new report warns that Staph bacteria are showing up in high rates at supermarkets.

A new report, saying that risky forms of Staph bacteria are showing up in supermarkets at "unexpectedly high rates," is raising concerns about whether the US meat and poultry industries are relying too heavily on antibiotic drugs.

Nearly half of meat and poultry samples in the nationwide study — 47 percent — were contaminated with Staphylococcus aureus, a bacteria that medical experts link to various human diseases. Of that amount, more than half the bacteria were resistant to at least three classes of antibiotics, according to the study by the Translational Genomics Research Institute in Phoenix.

The group said its findings raise concerns that widespread use of antibiotics in animal feed makes industrial farms breeding grounds for drug-resistant bacteria that can move from animals to humans.

“The fact that drug-resistant [Staph] was so prevalent, and likely came from the food animals themselves, is troubling, and demands attention to how antibiotics are used in food-animal production today,” Lance Price, senior author of the study, said in a statement released with the report.

Microbiology experts including Dr. Price worry that the rise in drug-resistant bacteria makes it harder to treat Staph-related diseases. The research institute notes that proper cooking kills the bacteria, although it can also pose a risk "through improper food handling and cross-contamination in the kitchen."

The study comes amid a wider debate about food safety and the potential risks of so-called industrial farming practices. Backers of organic foods hailed the report as a call for changing those practices, while some food-industry groups call the study into question.

“Calling into question the safety of U.S. beef without conclusive scientific evidence is careless and misleads consumers," the National Cattlemen's Beef Association said in a statement. "Pew Charitable Trusts, an agenda-driven organization on this issue, funded this study, which concludes that its extremely small sample size was ‘insufficient to accurately estimate prevalence rates’ and that ‘public health relevance of this finding is unclear.’ ”

The Translational Genomics Research Institute identifies itself as a nonprofit organization focused on researching medical diagnosis and treatments. It says its study, which was published in the journal Clinical Infectious Diseases, got grant funding from Pew's Campaign on Human Health and Industrial Farming.

Last year, the US Food and Drug Administration recommended phasing in measures to would limit the use of "medically important antimicrobial drugs" on US farms and ranches. The focus should be on "uses in food-producing animals that are considered necessary for assuring animal health."

The FDA guidance said that, so far, research generally supports the view that using the drugs to enhance animal growth "is not in the interest of protecting and promoting the public health."

In a blog post, writer Craig Goodwin called this week's study on Staph an "an important data point in the debate about the impact of antibiotic use in raising farm animals."

Mr. Goodwin is author of "Year of Plenty," a book about his family's experience during a year of relying on food that was locally or home grown. "The evidence is mounting that concentrated animal operations are not only bad for animals, but they are bad for humans as well," he said in the blog post.

Responding to such criticism, food-industry groups have said their practices are safe and keep food more affordably priced.

In a statement last year responding to the documentary film "Food, Inc.," the National Chicken Council said that "small-scale farms and ranches simply could not provide sufficient food for 300 million Americans and millions of other people around the world. There is simply not enough land or labor available to make the model work." It said the poultry industry's use of antibiotics "has declined."